I BF both my DSs, and experienced the same thing -- my right breast pumped 5+ ounces and my left 2-3 ounces. I never looked to do anything about it, because it didn't seem to cause any issue with BFing for us. I would always offer the other breast when he was finished with the first, and switched sides each time. I hope someone has some advice for you since it seems to be bothering you and your DS. I just wanted to let you know that I think it's pretty common.
Good luck!
Good luck!